Pyothorax-associated lymphoma (PAL) develops from a pyothorax caused by an artificial pneumothorax created during the treatment of pulmonary tuberculosis or tuberculous pleuritis. We report the first case of Epstein-Barr virus (EBV)-positive PAL arising from a posttraumatic empyema. A 75-year-old woman with chronic posttraumatic empyema presented with a tumor, which was connected to the wall of a pyothorax in the right thoracic cavity. She had a history of trauma to the right chest, which had occurred at the age of 45 years and had caused the chronic posttraumatic empyema. Pathological features of the resected tumor were conclusive for a diagnosis of EBV-positive PAL. Although neither postoperative chemotherapy nor radiotherapy was performed, remission was maintained for 3 years until recurrence in the liver. Combination chemotherapy led to complete remission, and 9 years after the initial diagnosis of PAL, the patient is still alive. An intriguing finding is the phenotypic alteration during the disease course. Although the primary tumor was negative for CD20 and CD3, the recurrent tumor expressed both of these molecules. We discuss this case of PAL, which was not a complication of lung tuberculosis, and the aberrant chronological phenotypic change observed in the lymphoma cells, and compare it with a usual case of PAL.